Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study

Abstract

Background: Antimalarial resistance is rapidly spreading across parts of southeast Asia where dihydroartemisinin-piperaquine is used as first-line treatment for Plasmodium falciparum malaria. The first published reports about resistance to antimalarial drugs came from western Cambodia in 2013. Here, we analyse genetic changes in the P falciparum population of western Cambodia in the 6 years before those reports.

Methods: We analysed genome sequence data on 1492 P falciparum samples from 11 locations across southeast Asia, including 464 samples collected in western Cambodia between 2007 and 2013. Different epidemiological origins of resistance were identified by haplotypic analysis of the kelch13 artemisinin resistance locus and the plasmepsin 2-3 piperaquine resistance locus.

Findings: We identified more than 30 independent origins of artemisinin resistance, of which the KEL1 lineage accounted for 140 (91%) of 154 parasites resistant to dihydroartemisinin-piperaquine. In 2008, KEL1 combined with PLA1, the major lineage associated with piperaquine resistance. By 2013, the KEL1/PLA1 co-lineage had reached a frequency of 63% (24/38) in western Cambodia and had spread to northern Cambodia.

Interpretation: The KEL1/PLA1 co-lineage emerged in the same year that dihydroartemisinin-piperaquine became the first-line antimalarial drug in western Cambodia and spread rapidly thereafter, displacing other artemisinin-resistant parasite lineages. These findings have important implications for management of the global health risk associated with the current outbreak of multidrug-resistant malaria in southeast Asia.

Funding: Wellcome Trust, Bill & Melinda Gates Foundation, Medical Research Council, UK Department for International Development, and the Intramural Research Program of the National Institute of Allergy and Infectious Diseases.

Figure 1

Cumulative frequency of kelch13 mutations (A) and haplogroups (B) Southeast Asia (east) includes northern and northeastern Cambodia, Vietnam, Laos, and northeastern Thailand. Southeast Asia (west) includes northwestern and southern Thailand and Myanmar.

Figure 2

Frequency of plasmepsin 2–3 (A) and mdr1 (B) amplifications Southeast Asia (east) includes northern and northeastern Cambodia, Vietnam, Laos, and northeastern Thailand. Southeast Asia (west) includes northwestern and southern Thailand and Myanmar.

Figure 3

Frequency in western Cambodia of molecular markers for the three most commonly used drugs in the area and of the KEL1 lineage from 2007 to 2013 (A) Cumulative frequency over time of kelch13 mutations, plasmepsin 2–3 amplifications, and mdr1 amplifications; error bars are 95% CIs of the frequencies, based on sample sizes. (B) Frequency over time of the dominant haplogroup KEL1; 22 samples in which the presence of either plasmepsin 2–3 or mdr1 amplifications could not be established reliably were excluded from the graph. *These parasites had only single copies of plasmepsin 2–3 and mdr1.

Figure 4

Spread of dihydroartemisinin–piperaquine resistance to north Cambodia (A) Each point represents a sample from northern Cambodia; bold lines indicate medians and thin lines indicate IQRs. (B) Genome-wide neighbour-joining tree of all samples from northern and western Cambodia in the dataset, with those carrying plasmepsin 2-3 amplifications identified by black dots at the tip. The circular subpanels show a magnified view of parts of the tree containing samples from northern Cambodia carrying plasmepsin 2–3 amplifications.